If you use keyboard, all keys (at least in My Keys plugin) still do their thing and removes focus from virtual keyboard. You have to do something that triggers virtual keyboard again to get rid of it, or else it stays on top.

Thats what i have done:
Bringing the virtual Keyboard on the screen e.g. when no IMDB-entry was found.

Push the "Green-Button" on the MCE-Remote or press "ESC" on the keyboard while you see the virtual keyboard.

MP goes back to the homescreen and the virtual keyboard looses his focus - so you still have the keyboard in
the foreground but when you move up or down with the remote or the real keyboard you move through the menu (no chance to close the Virtual keyboard).

The only way to get the focus back is to go to an point where you would bring back typically the virtual keyboard.